Rice, MD Anderson researchers win NIH grant to study protein networks

Researchers at Rice University and the University of Texas MD Anderson Cancer Center have received a $1.3 million grant from the National Institutes of Health to create processes that will look more deeply than ever into the protein networks that drive cells.

A federally funded collaboration between Rice University and the University of Texas MD Anderson Cancer Center will help researchers create processes to evaluate protein networks that regulate cells’ cytoskeletons. The researchers are integrating novel synthetic genetic regulation, super-resolution imaging and computational phenotyping methods to study and control the plasticity of cancer cells. Graphic by Amina Qutub/Rice University

The four-year grant to Rice bioengineers Michael Diehl and Amina Qutub and MD Anderson synthetic biologist Gábor Balázsi will enable a collaboration on new ways to see and evaluate the mechanisms that give cells their shapes, prompt them to change and move and sometimes help them evade safeguards and turn cancerous.

Each of the labs offers unique technology that when combined should let scientists analyze many characteristics of a cell at once. They will focus first on the internal cytoskeleton of stem cells and the proteins that regulate the cells’ plasticity, defined as their ability to take on the characteristics of other types of cells.

“This study is not as much about how cells change as about seeing how flexibly they can change their status and behaviors,” said Diehl, the project leader and an associate professor of bioengineering and of chemistry based at Rice’s BioScience Research Collaborative (BRC). “We want to develop a composite experimental and theoretical approach that allows one to take individual proteins and control their expression level uniformly in a population of cells.

“Then we can do two things: We can see if the cells move differently and their shapes change, and we can characterize the spatial patterning of cytoskeletal regulatory molecules. Correlating these behaviors and properties will allow us to find the sources of plasticity at the cellular and molecular level,” he said.

This image shows characteristics of a single cell that can be determined through processes developed at Rice. Images by Byron Long/Rice University

“The idea is that we can manipulate one of the proteins involved in a regulatory pathway so we can trigger cells to become more plastic,” said Qutub, an assistant professor of bioengineering at the BRC. She said the experiments could offer clues as to why some cells are more prone to turn cancerous than others.

The research will first focus on what are known as master cytoskeletal regulatory proteins (CRPs) that control how cells take shape and move. The overexpression of these proteins is known to be associated with poor prognosis for some cancer patients, but the researchers said their workings remain largely unknown.

Balázsi’s lab has developed the ability to prompt the expression of genetically modified proteins that give the researchers a level of control over CRPs with minimal disruption of other cell functions. This lets the researchers design experiments to see how the systems inside cells respond to stress.

Michael Diehl

Diehl is most interested in a CRP called “IQGAP.” “It both tunes cell-signaling responses and is involved in controlling proteins that regulate the cytoskeleton,” he said. “It’s at the junction of those two behaviors.” By perturbing the regulatory network through modified IQGAP, “we can look at the network response and correlate that with cellular behavior. It’s a very powerful approach that can be applied to many molecular and cellular processes.”

Diehl’s lab will view those processes with a multiplexed “super resolution” imaging technique that lets researchers see individual protein molecules inside cells in three dimensions. That will allow them to identify multiple proteins in a cell, perhaps hundreds, at once. Key to the technique is the ability to combine images that focus on different target proteins into a comprehensive picture of cellular structure.

“We have developed erasable molecular imaging probes for these types of studies,” Diehl said. Tagging proteins with fluorescent dyes allows researchers to “see” them, but current microscopes are limited to only a few color channels. With the ability to tag, erase and retag proteins, the Diehl lab can capture much more information from snapshots of a cell taken before and after perturbation.

Amina Qutub

Qutub’s lab analyzes protein-signaling pathways by integrating sophisticated image processing, statistical analysis and computer models to characterize the dynamic processes happening inside cells. The image-processing component lets researchers pick out dominant cells from a sample of as many as 40,000 within a few hours, she said.

Combined with Diehl’s super-resolution images, they will be able to see structures inside Balázsi’s engineered cells in great detail. “The images will give us 50 or 60 metrics that describe what a cell looks like, including chemical signaling,” Qutub said. “This will allow us to rapidly phenotype (or characterize) the cell.” Then, she said, her lab will build computer models to predict how cells of certain types will change.

Qutub said determining the nature of particular cells in a sample should become “like picking a person out of a crowd.

“We should be able to determine that over time a group of cells will include, say, four dominant phenotypes, or will have certain dynamics,” she said. The technique is promising for clinical biopsies to diagnose or compare patients, or even to see if a person is predisposed to a particular disease, she said. “All these techniques could be applied in the future to patient samples.”